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core filament of the spirochete periplasmic flagella of Leptospira biflexa wild type
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9LRZ
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 4.1836 f_angle_d 0.5949 f_chiral_restr 0.0379 f_plane_restr 0.0043 f_bond_d 0.0025
Sample core filament of the spirochete periplasmic flagella from wild type
Specimen Preparation Sample Aggregation State FILAMENT Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE Sample Vitrification Details
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 273749 Reported Resolution (Å) 4.35 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 (9LRZ) Refinement Space REAL Refinement Protocol RIGID BODY FIT Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type FEI FALCON III (4k x 4k) Electron Dose (electrons/Å**2) 50
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS KRIOS Minimum Defocus (nm) 500 Maximum Defocus (nm) 2000 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS 0.01 Imaging Mode BRIGHT FIELD Specimen Holder Model FEI TITAN KRIOS AUTOGRID HOLDER Nominal Magnification 59000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION cryoSPARC 4.2.1 IMAGE ACQUISITION EPU CTF CORRECTION cryoSPARC 4.2.1 MODEL FITTING Coot 0.9.8.7 INITIAL EULER ASSIGNMENT cryoSPARC 4.2.1 FINAL EULER ASSIGNMENT cryoSPARC 4.2.1 CLASSIFICATION cryoSPARC 4.2.1 RECONSTRUCTION cryoSPARC 4.2.1 MODEL REFINEMENT PHENIX 1.21.1_5286
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING ONLY